# HG changeset patch
# User devteam
# Date 1426790590 14400
# Node ID 67a4da1a4df3b05fff51115faf46545fb693f20c

Uploaded

diff -r 000000000000 -r 67a4da1a4df3 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Mar 19 14:43:10 2015 -0400
@@ -0,0 +1,28 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="8a5602bf07">vcflib</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" level="fatal" />
+        </stdio>
+    </xml>
+   	<xml name="citations">
+   	     <citations>
+             <citation type="bibtex">
+@misc{Garrison2015,
+  author = {Garrison, Erik},
+  year = {2015},
+  title = {vcflib},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/ekg/vcflib},
+}
+             </citation>
+   	     </citations>
+   	</xml>
+    <token name="@IS_PART_OF_VCFLIB@">is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).</token>
+</macros>
diff -r 000000000000 -r 67a4da1a4df3 test-data/vcflib-phix.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcflib-phix.vcf	Thu Mar 19 14:43:10 2015 -0400
@@ -0,0 +1,219 @@
+##fileformat=VCFv4.1
+##fileDate=20140610
+##source=Dan
+##reference=file:///galaxy/data/phiX/sam_index/phiX.fa
+##filter="AF > .001"
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	groupA	groupB
+phiX174	1015	.	A	C	0	.	AC=2;AF=0.0555555555556	GT:AC:AF:NC	0:0,2:0,0.2:A=8,C=2,G=1,	0:0,0:0,0:A=26,G=1,
+phiX174	1016	.	A	T	0	.	AC=2;AF=0.0555555555556	GT:AC:AF:NC	0:0:0:A=10,	0:2:0.0769230769231:A=24,T=2,
+phiX174	1038	.	A	C	0	.	AC=2;AF=0.046511627907	GT:AC:AF:NC	0:2:0.153846153846:A=11,C=2,	0:0:0:A=30,
+phiX174	1045	.	T	G	0	.	AC=2;AF=0.0425531914894	GT:AC:AF:NC	0:0:0:T=15,G=1,	0:2:0.0625:T=30,G=2,
+phiX174	1048	.	C	A	0	.	AC=2;AF=0.0434782608696	GT:AC:AF:NC	0:2:0.133333333333:A=2,C=13,	0:0:0:C=31,G=1,
+phiX174	1050	.	A	C	0	.	AC=3;AF=0.0714285714286	GT:AC:AF:NC	0:0:0:A=12,	0:3:0.1:A=27,C=3,
+phiX174	1051	.	T	G	0	.	AC=2;AF=0.0487804878049	GT:AC:AF:NC	0:2:0.166666666667:C=1,T=10,G=2,	0:0:0:T=29,G=1,
+phiX174	1054	.	T	G	0	.	AC=2;AF=0.0454545454545	GT:AC:AF:NC	0:2:0.153846153846:T=11,G=2,	0:0:0:T=31,G=1,
+phiX174	1076	.	G	C	0	.	AC=2;AF=0.0363636363636	GT:AC:AF:NC	0:2:0.105263157895:A=1,C=2,G=17,	0:0:0:G=36,
+phiX174	1080	.	G	C	0	.	AC=2;AF=0.0344827586207	GT:AC:AF:NC	0:2:0.105263157895:A=1,C=2,T=1,G=17,	0:0:0:C=1,G=39,
+phiX174	1092	.	T	G	0	.	AC=2;AF=0.0263157894737	GT:AC:AF:NC	0:2:0.0833333333333:C=1,T=22,G=2,	0:0:0:T=52,G=1,
+phiX174	1093	.	T	G	0	.	AC=2;AF=0.025974025974	GT:AC:AF:NC	0:2:0.08:T=23,G=2,	0:0:0:T=52,
+phiX174	1102	.	T	C	0	.	AC=6;AF=0.0779220779221	GT:AC:AF:NC	0:2:0.0869565217391:C=2,T=21,	0:4:0.0740740740741:C=4,T=50,
+phiX174	1107	.	T	G	0	.	AC=2;AF=0.0277777777778	GT:AC:AF:NC	0:0:0:T=22,G=1,	0:2:0.04:T=48,G=2,
+phiX174	1110	.	T	C	0	.	AC=2;AF=0.0277777777778	GT:AC:AF:NC	0:2:0.125:C=2,T=14,	0:0:0:C=1,T=56,G=1,
+phiX174	1121	.	T	G	0	.	AC=3;AF=0.041095890411	GT:AC:AF:NC	0:0:0:T=19,	0:3:0.0555555555556:T=51,G=3,
+phiX174	1124	.	T	C	0	.	AC=2;AF=0.0307692307692	GT:AC:AF:NC	0:0,2:0,0.117647058824:C=2,T=15,G=1,	0:0,0:0,0:T=48,G=1,
+phiX174	1125	.	T	G	0	.	AC=3;AF=0.0454545454545	GT:AC:AF:NC	0:3:0.176470588235:T=14,G=3,	0:0:0:T=49,G=1,
+phiX174	1131	.	T	G	0	.	AC=2;AF=0.025641025641	GT:AC:AF:NC	0:2:0.0952380952381:T=19,G=2,	0:0:0:T=57,
+phiX174	1141	.	T	G	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:0:0:T=20,G=1,	0:2:0.0338983050847:T=57,G=2,
+phiX174	1145	.	G	C	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:2:0.0952380952381:C=2,G=19,	0:0:0:G=52,
+phiX174	1147	.	T	C	0	.	AC=2;AF=0.0281690140845	GT:AC:AF:NC	0:2:0.0952380952381:C=2,T=19,	0:0:0:T=50,
+phiX174	1149	.	T	G,C	0	.	AC=2,2;AF=0.027027027027,0.027027027027	GT:AC:AF:NC	0:2,2:0.1,0.1:C=2,T=16,G=2,	0:0,0:0,0:T=54,
+phiX174	1156	.	T	G	0	.	AC=2;AF=0.031746031746	GT:AC:AF:NC	0:0:0:C=1,T=15,	0:2:0.0416666666667:T=46,G=2,
+phiX174	1159	.	T	C,G	0	.	AC=2,2;AF=0.0298507462687,0.0298507462687	GT:AC:AF:NC	0:2,0:0.111111111111,0:C=2,T=16,	0:0,2:0,0.0408163265306:C=1,T=47,G=2,
+phiX174	1164	.	T	G	0	.	AC=4;AF=0.0666666666667	GT:AC:AF:NC	0:0:0:C=1,T=16,G=1,	0:4:0.0909090909091:T=40,G=4,
+phiX174	1168	.	T	G	0	.	AC=4;AF=0.0666666666667	GT:AC:AF:NC	0:2:0.0952380952381:C=1,T=19,G=2,	0:2:0.0512820512821:T=37,G=2,
+phiX174	1171	.	T	G	0	.	AC=2;AF=0.0327868852459	GT:AC:AF:NC	0:2:0.0869565217391:T=21,G=2,	0:0:0:T=38,G=1,
+phiX174	1174	.	C	A	0	.	AC=2;AF=0.0327868852459	GT:AC:AF:NC	0:2:0.0869565217391:A=2,C=21,	0:0:0:A=1,C=38,
+phiX174	1178	.	G	C	0	.	AC=2;AF=0.0307692307692	GT:AC:AF:NC	0:2:0.0740740740741:C=2,T=1,G=25,	0:0:0:G=38,
+phiX174	1187	.	T	G	0	.	AC=3;AF=0.04	GT:AC:AF:NC	0:3:0.0882352941176:C=1,T=31,G=3,	0:0:0:T=41,
+phiX174	1189	.	T	C	0	.	AC=3;AF=0.0379746835443	GT:AC:AF:NC	0:3:0.0857142857143:C=3,T=32,G=1,	0:0:0:T=44,
+phiX174	1200	.	T	G	0	.	AC=3;AF=0.0365853658537	GT:AC:AF:NC	0:3:0.0882352941176:T=31,G=3,	0:0:0:T=48,G=1,
+phiX174	1202	.	T	G	0	.	AC=3;AF=0.0365853658537	GT:AC:AF:NC	0:0:0:T=32,	0:3:0.06:T=47,G=3,
+phiX174	1205	.	A	C	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:2:0.0588235294118:A=32,C=2,	0:0:0:A=47,C=1,G=1,
+phiX174	1207	.	T	G	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:0:0:A=1,T=34,	0:2:0.0425531914894:T=45,G=2,
+phiX174	1214	.	G	A	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:0:0:T=1,G=34,	0:2:0.0425531914894:A=2,G=45,
+phiX174	1216	.	C	A	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:0:0:C=34,	0:2:0.0425531914894:A=2,C=45,
+phiX174	1217	.	C	A	0	.	AC=2;AF=0.025	GT:AC:AF:NC	0:2:0.0588235294118:A=2,C=32,	0:0:0:C=46,
+phiX174	1219	.	T	G	0	.	AC=2;AF=0.025641025641	GT:AC:AF:NC	0:0:0:C=1,T=33,G=1,	0:2:0.0444444444444:T=43,G=2,
+phiX174	1223	.	C	T	0	.	AC=2;AF=0.025	GT:AC:AF:NC	0:2:0.0555555555556:C=34,T=2,	0:0:0:C=44,
+phiX174	1227	.	A	C	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:2:0.0588235294118:A=32,C=2,	0:0:0:A=40,
+phiX174	1232	.	T	G	0	.	AC=2;AF=0.0298507462687	GT:AC:AF:NC	0:0:0:T=34,	0:2:0.0606060606061:C=1,T=31,G=2,
+phiX174	1236	.	G	T	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:2:0.0606060606061:A=1,T=2,G=31,	0:0:0:G=35,
+phiX174	1237	.	T	G	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:2:0.0571428571429:A=1,T=33,G=2,	0:0:0:T=33,G=1,
+phiX174	1240	.	A	C	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:0,0:0,0:A=32,T=1,	0:0,2:0,0.0555555555556:A=34,C=2,T=1,
+phiX174	1245	.	G	T	0	.	AC=4;AF=0.0625	GT:AC:AF:NC	0:2:0.0666666666667:C=1,T=2,G=28,	0:2:0.0588235294118:T=2,G=32,
+phiX174	1247	.	A	T	0	.	AC=2;AF=0.031746031746	GT:AC:AF:NC	0:2:0.0714285714286:A=26,C=1,T=2,G=1,	0:0:0:A=35,
+phiX174	1250	.	A	C	0	.	AC=2;AF=0.0307692307692	GT:AC:AF:NC	0:2:0.0769230769231:A=24,C=2,	0:0:0:A=39,
+phiX174	1251	.	A	G	0	.	AC=3;AF=0.044776119403	GT:AC:AF:NC	0:0:0:A=29,	0:3:0.0789473684211:A=35,C=1,G=3,
+phiX174	1253	.	T	G	0	.	AC=4;AF=0.0526315789474	GT:AC:AF:NC	0:2:0.0645161290323:T=29,G=2,	0:2:0.0444444444444:T=43,G=2,
+phiX174	1257	.	T	G	0	.	AC=2;AF=0.0281690140845	GT:AC:AF:NC	0:0:0:T=26,	0:2:0.0444444444444:T=43,G=2,
+phiX174	1259	.	A	C	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:0:0:A=28,T=1,	0:2:0.0444444444444:A=43,C=2,G=1,
+phiX174	1274	.	G	C	0	.	AC=2;AF=0.0240963855422	GT:AC:AF:NC	0:2:0.0512820512821:C=2,G=37,	0:0:0:G=44,
+phiX174	1277	.	A	C	0	.	AC=2;AF=0.025	GT:AC:AF:NC	0:2:0.05:A=38,C=2,	0:0:0:A=40,G=1,
+phiX174	1279	.	T	G	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:0:0:T=39,G=1,	0:2:0.05:C=1,T=38,G=2,
+phiX174	1284	.	T	G,C	0	.	AC=3,2;AF=0.038961038961,0.025974025974	GT:AC:AF:NC	0:3,2:0.075,0.05:C=2,T=35,G=3,	0:0,0:0,0:A=1,T=37,
+phiX174	1289	.	A	C	0	.	AC=3;AF=0.0454545454545	GT:AC:AF:NC	0:3:0.0789473684211:A=35,C=3,	0:0:0:A=28,G=1,
+phiX174	1296	.	A	C	0	.	AC=2;AF=0.03125	GT:AC:AF:NC	0:0:0:A=38,	0:2:0.0769230769231:A=24,C=2,
+phiX174	1298	.	A	C	0	.	AC=3;AF=0.0491803278689	GT:AC:AF:NC	0:3,0:0.0810810810811,0:A=34,C=3,G=1,	0:0,0:0,0:A=24,C=1,T=1,G=1,
+phiX174	1306	.	T	G	0	.	AC=5;AF=0.0943396226415	GT:AC:AF:NC	0:5:0.178571428571:T=23,G=5,	0:0:0:C=1,T=25,
+phiX174	1307	.	T	G	0	.	AC=3;AF=0.0545454545455	GT:AC:AF:NC	0:3:0.107142857143:T=25,G=3,	0:0:0:C=1,T=27,
+phiX174	1314	.	A	G	0	.	AC=5;AF=0.0877192982456	GT:AC:AF:NC	0:2,0:0.0740740740741,0:A=25,C=1,G=2,	0:3,0:0.1,0:A=27,C=1,G=3,
+phiX174	1317	.	A	C	0	.	AC=2;AF=0.0322580645161	GT:AC:AF:NC	0:2:0.0740740740741:A=25,C=2,	0:0:0:A=35,
+phiX174	1320	.	C	G	0	.	AC=2;AF=0.0322580645161	GT:AC:AF:NC	0:2:0.0769230769231:C=24,G=2,	0:0:0:C=36,
+phiX174	1322	.	G	C	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:3:0.107142857143:C=3,G=25,	0:0:0:G=40,
+phiX174	1323	.	C	G	0	.	AC=2;AF=0.0298507462687	GT:AC:AF:NC	0:0:0:C=28,	0:2:0.0512820512821:C=37,T=1,G=2,
+phiX174	1329	.	T	C	0	.	AC=2;AF=0.0277777777778	GT:AC:AF:NC	0:2:0.0666666666667:C=2,T=28,	0:0:0:T=42,G=1,
+phiX174	1335	.	C	A	0	.	AC=2;AF=0.025974025974	GT:AC:AF:NC	0:2:0.0625:A=2,C=30,	0:0:0:C=45,
+phiX174	1338	.	T	A	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:0:0:T=32,	0:2:0.047619047619:A=2,T=40,
+phiX174	1345	.	T	C	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:0,0:0,0:T=36,G=1,	0:0,2:0,0.046511627907:C=2,T=41,G=1,
+phiX174	1347	.	A	C	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0512820512821:A=37,C=2,G=1,	0:0:0:A=43,
+phiX174	1348	.	T	G	0	.	AC=2;AF=0.0240963855422	GT:AC:AF:NC	0:2:0.05:T=38,G=2,	0:0:0:T=43,
+phiX174	1352	.	A	T	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:0:0:A=34,G=1,	0:2:0.0512820512821:A=37,T=2,
+phiX174	1354	.	T	G,A	0	.	AC=2,2;AF=0.027027027027,0.027027027027	GT:AC:AF:NC	0:2,0:0.0526315789474,0:T=36,G=2,	0:0,2:0,0.0555555555556:A=2,T=34,G=1,
+phiX174	1359	.	T	G	0	.	AC=3;AF=0.0405405405405	GT:AC:AF:NC	0:3:0.0714285714286:T=39,G=3,	0:0:0:T=32,G=1,
+phiX174	1366	.	G	C	0	.	AC=3;AF=0.0428571428571	GT:AC:AF:NC	0:3:0.0714285714286:C=3,T=1,G=39,	0:0:0:G=28,
+phiX174	1370	.	T	G	0	.	AC=2;AF=0.0289855072464	GT:AC:AF:NC	0:0:0:C=1,T=45,G=1,	0:2:0.0833333333333:A=1,T=22,G=2,
+phiX174	1373	.	T	G	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:2:0.0408163265306:T=47,G=2,	0:0:0:T=25,
+phiX174	1380	.	G	C	0	.	AC=2;AF=0.0238095238095	GT:AC:AF:NC	0:0,2:0,0.0384615384615:C=2,T=1,G=50,	0:0,0:0,0:T=1,G=32,
+phiX174	1381	.	T	G	0	.	AC=3;AF=0.0361445783133	GT:AC:AF:NC	0:3:0.0576923076923:A=1,T=49,G=3,	0:0:0:T=31,
+phiX174	1384	.	T	G	0	.	AC=4;AF=0.0512820512821	GT:AC:AF:NC	0:4:0.0816326530612:T=45,G=4,	0:0:0:T=29,G=1,
+phiX174	1385	.	T	G	0	.	AC=4;AF=0.0512820512821	GT:AC:AF:NC	0:4:0.0816326530612:T=45,G=4,	0:0:0:C=1,T=29,
+phiX174	1391	.	A	C	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:2:0.0408163265306:A=47,C=2,	0:0:0:A=30,C=1,
+phiX174	1393	.	C	A	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:2:0.0425531914894:A=2,C=45,	0:0:0:C=32,
+phiX174	1396	.	T	G	0	.	AC=3;AF=0.04	GT:AC:AF:NC	0:3:0.0697674418605:T=40,G=3,	0:0:0:T=32,
+phiX174	1397	.	A	C	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:0:0:A=42,T=1,	0:2:0.0625:A=30,C=2,
+phiX174	1400	.	A	C	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:2:0.047619047619:A=40,C=2,G=1,	0:0:0:A=31,
+phiX174	1401	.	A	C	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:2:0.047619047619:A=40,C=2,	0:0:0:A=31,
+phiX174	1434	.	C	T	0	.	AC=2;AF=0.0571428571429	GT:AC:AF:NC	0:2:0.142857142857:C=12,T=2,	0:0:0:C=21,
+phiX174	1438	.	G	C	0	.	AC=2;AF=0.0526315789474	GT:AC:AF:NC	0:0:0:G=15,	0:2:0.0869565217391:C=2,G=21,
+phiX174	1450	.	T	G	0	.	AC=3;AF=0.0789473684211	GT:AC:AF:NC	0:3:0.176470588235:A=1,C=1,T=14,G=3,	0:0:0:T=21,G=1,
+phiX174	1459	.	T	G	0	.	AC=3;AF=0.075	GT:AC:AF:NC	0:3:0.142857142857:C=1,T=18,G=3,	0:0:0:T=19,
+phiX174	1470	.	C	A	0	.	AC=2;AF=0.0384615384615	GT:AC:AF:NC	0:0:0:C=29,	0:2:0.0869565217391:A=2,C=21,
+phiX174	1484	.	C	G	0	.	AC=2;AF=0.0384615384615	GT:AC:AF:NC	0:2:0.0740740740741:A=1,C=25,G=2,	0:0:0:C=25,
+phiX174	1487	.	T	G	0	.	AC=2;AF=0.0363636363636	GT:AC:AF:NC	0:2:0.0689655172414:T=27,G=2,	0:0:0:T=26,
+phiX174	1491	.	G	T	0	.	AC=2;AF=0.037037037037	GT:AC:AF:NC	0:0:0:T=1,G=26,	0:2:0.0714285714286:T=2,G=26,
+phiX174	1503	.	A	C	0	.	AC=2;AF=0.0454545454545	GT:AC:AF:NC	0:0:0:A=20,C=1,	0:2:0.0833333333333:A=22,C=2,
+phiX174	1536	.	A	C	0	.	AC=3;AF=0.0545454545455	GT:AC:AF:NC	0:3:0.111111111111:A=24,C=3,	0:0:0:A=28,C=1,
+phiX174	1541	.	T	G	0	.	AC=2;AF=0.0363636363636	GT:AC:AF:NC	0:2:0.0740740740741:T=25,G=2,	0:0:0:T=28,
+phiX174	1553	.	A	G	0	.	AC=2;AF=0.0408163265306	GT:AC:AF:NC	0:2:0.0952380952381:A=19,C=1,G=2,	0:0:0:A=28,
+phiX174	1566	.	C	G	0	.	AC=2;AF=0.0307692307692	GT:AC:AF:NC	0:0:0:C=30,T=1,	0:2:0.0571428571429:C=33,G=2,
+phiX174	1572	.	T	G	0	.	AC=2;AF=0.03125	GT:AC:AF:NC	0:2:0.0625:T=30,G=2,	0:0:0:T=32,
+phiX174	1574	.	G	C	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:3:0.0882352941176:C=3,G=31,	0:0:0:G=34,
+phiX174	1575	.	A	C	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:2:0.0571428571429:A=33,C=2,	0:0:0:A=33,T=1,
+phiX174	1577	.	A	C	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:0:0:A=35,	0:3:0.0909090909091:A=30,C=3,
+phiX174	1581	.	T	G	0	.	AC=2;AF=0.0285714285714	GT:AC:AF:NC	0:2:0.0555555555556:C=1,T=34,G=2,	0:0:0:T=34,G=1,
+phiX174	1591	.	A	C	0	.	AC=3;AF=0.037037037037	GT:AC:AF:NC	0:3:0.0789473684211:A=35,C=3,	0:0:0:A=43,C=1,
+phiX174	1597	.	T	G	0	.	AC=2;AF=0.025641025641	GT:AC:AF:NC	0:2:0.0606060606061:T=31,G=2,	0:0:0:C=1,T=45,
+phiX174	1603	.	T	G	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0625:T=30,G=2,	0:0:0:T=50,
+phiX174	1606	.	T	G	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0666666666667:A=1,C=1,T=28,G=2,	0:0:0:T=52,
+phiX174	1611	.	A	C	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0769230769231:A=24,C=2,	0:0:0:A=56,C=1,
+phiX174	1613	.	A	G	0	.	AC=2;AF=0.0240963855422	GT:AC:AF:NC	0:0:0:A=25,C=1,G=1,	0:2:0.0344827586207:A=56,G=2,
+phiX174	1618	.	C	A	0	.	AC=2;AF=0.0229885057471	GT:AC:AF:NC	0:2:0.0666666666667:A=2,C=28,G=1,	0:0:0:A=1,C=57,
+phiX174	1619	.	C	A	0	.	AC=2;AF=0.0229885057471	GT:AC:AF:NC	0:2:0.0666666666667:A=2,C=28,	0:0:0:C=57,
+phiX174	1621	.	A	C	0	.	AC=3;AF=0.0352941176471	GT:AC:AF:NC	0:0:0:A=31,T=1,G=1,	0:3:0.0555555555556:A=51,C=3,
+phiX174	1622	.	G	T	0	.	AC=2;AF=0.0224719101124	GT:AC:AF:NC	0:0:0:A=1,G=35,	0:2:0.037037037037:T=2,G=52,
+phiX174	1624	.	A	G	0	.	AC=2;AF=0.0235294117647	GT:AC:AF:NC	0:2:0.0555555555556:A=34,T=1,G=2,	0:0:0:A=49,
+phiX174	1627	.	T	G,C	0	.	AC=2,2;AF=0.0246913580247,0.0246913580247	GT:AC:AF:NC	0:0,0:0,0:T=37,G=1,	0:2,2:0.0454545454545,0.0454545454545:C=2,T=40,G=2,
+phiX174	1630	.	T	G	0	.	AC=2;AF=0.025641025641	GT:AC:AF:NC	0:2:0.0526315789474:C=1,T=36,G=2,	0:0:0:T=40,
+phiX174	1632	.	A	C	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:2:0.05:A=38,C=2,	0:0:0:A=41,
+phiX174	1634	.	T	G	0	.	AC=4;AF=0.0493827160494	GT:AC:AF:NC	0:2:0.047619047619:C=1,T=40,G=2,	0:2:0.0512820512821:T=37,G=2,
+phiX174	1635	.	T	G	0	.	AC=3;AF=0.0365853658537	GT:AC:AF:NC	0:3:0.0714285714286:T=39,G=3,	0:0:0:T=40,
+phiX174	1639	.	G	A	0	.	AC=3;AF=0.0405405405405	GT:AC:AF:NC	0:3:0.075:A=3,T=1,G=37,	0:0:0:G=34,
+phiX174	1645	.	T	G	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:2:0.0425531914894:T=45,G=2,	0:0:0:T=27,G=1,
+phiX174	1647	.	A	T,G,C	0	.	AC=2,2,2;AF=0.0253164556962,0.0253164556962,0.0253164556962	GT:AC:AF:NC	0:0,2,2:0,0.0384615384615,0.0384615384615:A=48,C=2,G=2,	0:2,0,0:0.0740740740741,0,0:A=25,T=2,
+phiX174	1652	.	G	A	0	.	AC=2;AF=0.0240963855422	GT:AC:AF:NC	0:2:0.037037037037:A=2,G=52,	0:0:0:G=29,
+phiX174	1656	.	T	G	0	.	AC=3;AF=0.0348837209302	GT:AC:AF:NC	0:3:0.0555555555556:T=51,G=3,	0:0:0:T=32,G=1,
+phiX174	1658	.	A	C	0	.	AC=2;AF=0.0240963855422	GT:AC:AF:NC	0:2:0.04:A=48,C=2,	0:0:0:A=33,
+phiX174	1659	.	T	G	0	.	AC=3;AF=0.0365853658537	GT:AC:AF:NC	0:3:0.0625:C=1,T=45,G=3,	0:0:0:T=34,
+phiX174	1663	.	T	G	0	.	AC=4;AF=0.0454545454545	GT:AC:AF:NC	0:0:0:A=1,T=53,	0:4:0.114285714286:T=31,G=4,
+phiX174	1665	.	C	A	0	.	AC=2;AF=0.0212765957447	GT:AC:AF:NC	0:2:0.0384615384615:A=2,C=50,G=1,	0:0:0:C=42,
+phiX174	1670	.	G	C	0	.	AC=2;AF=0.0224719101124	GT:AC:AF:NC	0:0,2:0,0.0408163265306:A=1,C=2,T=1,G=47,	0:0,0:0,0:T=1,G=40,
+phiX174	1671	.	G	T	0	.	AC=2;AF=0.0212765957447	GT:AC:AF:NC	0:2:0.0384615384615:C=1,T=2,G=50,	0:0:0:G=42,
+phiX174	1672	.	A	G	0	.	AC=3;AF=0.0315789473684	GT:AC:AF:NC	0:3:0.0545454545455:A=52,G=3,	0:0:0:A=40,T=1,
+phiX174	1673	.	G	T	0	.	AC=2;AF=0.0212765957447	GT:AC:AF:NC	0:2:0.0377358490566:C=1,T=2,G=51,	0:0:0:G=41,
+phiX174	1674	.	G	T	0	.	AC=4;AF=0.04	GT:AC:AF:NC	0:4:0.0714285714286:T=4,G=52,	0:0:0:G=44,
+phiX174	1677	.	A	C	0	.	AC=3;AF=0.031914893617	GT:AC:AF:NC	0:3:0.0566037735849:A=50,C=3,N=1,	0:0:0:A=41,
+phiX174	1678	.	A	C	0	.	AC=2;AF=0.0212765957447	GT:AC:AF:NC	0:0:0:A=54,C=1,G=1,	0:2:0.05:A=38,C=2,
+phiX174	1682	.	T	C	0	.	AC=2;AF=0.0229885057471	GT:AC:AF:NC	0:2:0.0408163265306:C=2,T=47,G=1,	0:0:0:C=1,T=38,
+phiX174	1685	.	T	G	0	.	AC=2;AF=0.0238095238095	GT:AC:AF:NC	0:2:0.046511627907:A=1,T=41,G=2,	0:0:0:T=41,G=1,
+phiX174	1686	.	A	C	0	.	AC=2;AF=0.025641025641	GT:AC:AF:NC	0:0:0:A=39,C=1,T=1,G=1,	0:2:0.0512820512821:A=37,C=2,
+phiX174	1687	.	T	C	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.047619047619:C=2,T=40,	0:0:0:A=1,T=40,
+phiX174	1688	.	G	C	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:2:0.05:C=2,T=1,G=38,	0:0:0:G=41,
+phiX174	1689	.	A	C	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0487804878049:A=39,C=2,T=1,G=1,	0:0:0:A=41,C=1,
+phiX174	1691	.	G	C	0	.	AC=2;AF=0.025974025974	GT:AC:AF:NC	0:2:0.05:C=2,T=1,G=38,	0:0:0:G=37,
+phiX174	1693	.	T	G	0	.	AC=2;AF=0.0238095238095	GT:AC:AF:NC	0:0:0:T=42,G=1,	0:2:0.047619047619:T=40,G=2,
+phiX174	1695	.	A	C	0	.	AC=2;AF=0.0232558139535	GT:AC:AF:NC	0:2:0.046511627907:A=41,C=2,	0:0:0:A=43,C=1,
+phiX174	1702	.	T	C	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:2:0.0512820512821:A=1,C=2,T=37,	0:0:0:C=1,T=42,
+phiX174	1707	.	T	C	0	.	AC=2;AF=0.0232558139535	GT:AC:AF:NC	0:2:0.05:C=2,T=38,	0:0:0:T=46,G=1,
+phiX174	1708	.	A	C	0	.	AC=2;AF=0.0238095238095	GT:AC:AF:NC	0:2:0.0526315789474:A=36,C=2,	0:0:0:A=46,C=1,G=1,
+phiX174	1710	.	T	C	0	.	AC=2;AF=0.025	GT:AC:AF:NC	0:0:0:C=1,T=34,	0:2:0.0434782608696:C=2,T=44,
+phiX174	1723	.	T	C	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0588235294118:C=2,T=32,	0:0:0:T=48,
+phiX174	1724	.	A	C	0	.	AC=4;AF=0.0481927710843	GT:AC:AF:NC	0:2:0.0571428571429:A=33,C=2,	0:2:0.0416666666667:A=46,C=2,
+phiX174	1725	.	A	C	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0606060606061:A=31,C=2,	0:0:0:A=49,
+phiX174	1726	.	T	G	0	.	AC=3;AF=0.037037037037	GT:AC:AF:NC	0:3:0.0882352941176:T=31,G=3,	0:0:0:C=1,T=47,
+phiX174	1730	.	T	G	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:0:0:C=1,T=28,	0:2:0.0444444444444:T=43,G=2,
+phiX174	1739	.	G	T	0	.	AC=3;AF=0.0434782608696	GT:AC:AF:NC	0:3:0.09375:T=3,G=29,	0:0:0:G=37,
+phiX174	1746	.	A	C	0	.	AC=2;AF=0.0338983050847	GT:AC:AF:NC	0:2:0.0689655172414:A=27,C=2,	0:0:0:A=30,C=1,G=1,
+phiX174	1749	.	T	G,C	0	.	AC=3,2;AF=0.044776119403,0.0298507462687	GT:AC:AF:NC	0:3,2:0.0857142857143,0.0571428571429:C=2,T=30,G=3,	0:0,0:0,0:T=32,G=1,
+phiX174	1755	.	G	C	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:2:0.05:C=2,G=38,	0:0:0:C=1,G=33,
+phiX174	1756	.	A	G,C	0	.	AC=2,2;AF=0.0281690140845,0.0281690140845	GT:AC:AF:NC	0:0,2:0,0.0526315789474:A=36,C=2,T=1,G=1,	0:2,0:0.0606060606061,0:A=31,C=1,G=2,
+phiX174	1761	.	A	G	0	.	AC=2;AF=0.0285714285714	GT:AC:AF:NC	0:2:0.0512820512821:A=37,C=1,G=2,	0:0:0:A=31,
+phiX174	1764	.	A	C	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:2:0.05:A=38,C=2,	0:0:0:A=28,
+phiX174	1766	.	A	C	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:2:0.0487804878049:A=39,C=2,	0:0:0:A=27,
+phiX174	1769	.	T	G	0	.	AC=2;AF=0.03125	GT:AC:AF:NC	0:2:0.0526315789474:A=1,C=1,T=36,G=2,	0:0:0:T=26,G=1,
+phiX174	1771	.	G	C	0	.	AC=2;AF=0.0298507462687	GT:AC:AF:NC	0:2:0.0526315789474:C=2,G=36,	0:0:0:G=29,
+phiX174	1772	.	T	G	0	.	AC=4;AF=0.0597014925373	GT:AC:AF:NC	0:4:0.108108108108:C=1,T=33,G=4,	0:0:0:T=30,
+phiX174	1774	.	A	G	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:3:0.0810810810811:A=34,G=3,	0:0:0:A=31,
+phiX174	1775	.	G	A	0	.	AC=2;AF=0.030303030303	GT:AC:AF:NC	0:2:0.0571428571429:A=2,G=33,	0:0:0:G=31,
+phiX174	1776	.	G	T	0	.	AC=2;AF=0.0289855072464	GT:AC:AF:NC	0:2:0.0540540540541:T=2,G=35,	0:0:0:G=32,
+phiX174	1778	.	C	G	0	.	AC=2;AF=0.0289855072464	GT:AC:AF:NC	0:2:0.0526315789474:C=36,G=2,	0:0:0:C=31,
+phiX174	1779	.	A	C	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:3:0.075:A=37,C=3,	0:0:0:A=28,
+phiX174	1781	.	T	G	0	.	AC=5;AF=0.0714285714286	GT:AC:AF:NC	0:2:0.0487804878049:C=1,T=39,G=2,	0:3:0.103448275862:T=26,G=3,
+phiX174	1782	.	T	G	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:3:0.075:T=37,G=3,	0:0:0:A=1,T=28,
+phiX174	1783	.	T	C	0	.	AC=2;AF=0.0298507462687	GT:AC:AF:NC	0:2:0.0512820512821:C=2,T=37,	0:0:0:T=28,G=1,
+phiX174	1788	.	G	T	0	.	AC=2;AF=0.0344827586207	GT:AC:AF:NC	0:0:0:A=1,T=1,G=29,	0:2:0.0689655172414:T=2,G=27,
+phiX174	1792	.	T	G	0	.	AC=2;AF=0.0344827586207	GT:AC:AF:NC	0:2:0.0606060606061:T=31,G=2,	0:0:0:T=25,G=1,
+phiX174	1802	.	A	C	0	.	AC=2;AF=0.030303030303	GT:AC:AF:NC	0:2:0.0571428571429:A=33,C=2,	0:0:0:A=31,C=1,
+phiX174	1804	.	C	T	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:2:0.0588235294118:A=1,C=32,T=2,	0:0:0:C=34,
+phiX174	1805	.	T	G	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:3:0.0857142857143:T=32,G=3,	0:0:0:T=33,G=1,
+phiX174	1806	.	A	C	0	.	AC=2;AF=0.0289855072464	GT:AC:AF:NC	0:2:0.0571428571429:A=33,C=2,	0:0:0:A=34,G=1,
+phiX174	1824	.	G	C	0	.	AC=2;AF=0.0281690140845	GT:AC:AF:NC	0:2:0.0714285714286:C=2,T=1,G=26,	0:0:0:G=43,
+phiX174	1825	.	T	G	0	.	AC=2;AF=0.0281690140845	GT:AC:AF:NC	0:2:0.0689655172414:T=27,G=2,	0:0:0:T=42,G=1,
+phiX174	1833	.	T	G	0	.	AC=2;AF=0.0289855072464	GT:AC:AF:NC	0:0:0:A=1,T=24,	0:2:0.0444444444444:T=43,G=2,
+phiX174	1843	.	T	G	0	.	AC=2;AF=0.031746031746	GT:AC:AF:NC	0:2:0.08:A=1,T=23,G=2,	0:0:0:T=38,
+phiX174	1847	.	A	C	0	.	AC=2;AF=0.0333333333333	GT:AC:AF:NC	0:2:0.0833333333333:A=22,C=2,T=1,G=1,	0:0:0:A=36,
+phiX174	1854	.	T	G	0	.	AC=2;AF=0.0298507462687	GT:AC:AF:NC	0:0:0:T=26,	0:2:0.0487804878049:T=39,G=2,
+phiX174	1860	.	T	G	0	.	AC=2;AF=0.0377358490566	GT:AC:AF:NC	0:0:0:A=1,T=20,	0:2:0.0606060606061:T=31,G=2,
+phiX174	1863	.	C	G	0	.	AC=2;AF=0.0384615384615	GT:AC:AF:NC	0:2:0.105263157895:A=1,C=17,G=2,	0:0:0:C=33,
+phiX174	1866	.	T	G	0	.	AC=2;AF=0.04	GT:AC:AF:NC	0:0:0:T=19,G=1,	0:2:0.0645161290323:T=29,G=2,
+phiX174	1875	.	T	A	0	.	AC=2;AF=0.0377358490566	GT:AC:AF:NC	0:2:0.0952380952381:A=2,T=19,	0:0:0:T=32,G=1,
+phiX174	1876	.	T	G	0	.	AC=3;AF=0.0588235294118	GT:AC:AF:NC	0:3:0.157894736842:C=1,T=16,G=3,	0:0:0:T=32,G=1,
+phiX174	1882	.	T	G	0	.	AC=2;AF=0.0377358490566	GT:AC:AF:NC	0:2:0.105263157895:T=17,G=2,	0:0:0:T=34,
+phiX174	1889	.	A	C	0	.	AC=2;AF=0.04	GT:AC:AF:NC	0:2:0.0869565217391:A=21,C=2,	0:0:0:A=27,
+phiX174	1913	.	G	C	0	.	AC=2;AF=0.04	GT:AC:AF:NC	0:0:0:G=27,	0:2:0.0869565217391:C=2,G=21,
+phiX174	1915	.	T	G	0	.	AC=2;AF=0.0425531914894	GT:AC:AF:NC	0:0:0:A=1,T=24,	0:2:0.0869565217391:T=21,G=2,
+phiX174	1917	.	A	T	0	.	AC=2;AF=0.0444444444444	GT:AC:AF:NC	0:2,0:0.0833333333333,0:A=22,T=2,G=1,	0:0,0:0,0:A=21,G=1,
+phiX174	1930	.	T	A	0	.	AC=2;AF=0.0526315789474	GT:AC:AF:NC	0:2:0.0909090909091:A=2,T=20,	0:0:0:T=16,
+phiX174	1934	.	A	C	0	.	AC=2;AF=0.0512820512821	GT:AC:AF:NC	0:2:0.0952380952381:A=19,C=2,T=1,	0:0:0:A=18,C=1,
+phiX174	1940	.	A	C	0	.	AC=2;AF=0.046511627907	GT:AC:AF:NC	0:2:0.0952380952381:A=19,C=2,	0:0:0:A=22,C=1,
+phiX174	1942	.	T	G	0	.	AC=2;AF=0.047619047619	GT:AC:AF:NC	0:0:0:T=19,	0:2:0.0869565217391:T=21,G=2,
+phiX174	1945	.	T	G	0	.	AC=3;AF=0.0769230769231	GT:AC:AF:NC	0:0:0:T=15,G=1,	0:3:0.125:T=21,G=3,
+phiX174	1954	.	T	C	0	.	AC=2;AF=0.0625	GT:AC:AF:NC	0:0,0:0,0:T=12,G=1,	0:0,2:0,0.1:C=2,T=18,G=1,
+phiX174	1959	.	T	G	0	.	AC=2;AF=0.0555555555556	GT:AC:AF:NC	0:2:0.153846153846:T=11,G=2,	0:0:0:T=23,
+phiX174	1994	.	A	C	0	.	AC=2;AF=0.0512820512821	GT:AC:AF:NC	0:2:0.153846153846:A=11,C=2,	0:0:0:A=26,
+phiX174	1998	.	A	G	0	.	AC=2;AF=0.05	GT:AC:AF:NC	0:2:0.142857142857:A=12,G=2,	0:0:0:A=26,
diff -r 000000000000 -r 67a4da1a4df3 test-data/vcflib-test-genome-phix.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcflib-test-genome-phix.fa	Thu Mar 19 14:43:10 2015 -0400
@@ -0,0 +1,2 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCgTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
diff -r 000000000000 -r 67a4da1a4df3 test-data/vcfprimers-test1.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcfprimers-test1.fasta	Thu Mar 19 14:43:10 2015 -0400
@@ -0,0 +1,828 @@
+>phiX174_1015_LEFT
+ATTCA
+>phiX174_1015_RIGHT
+ACTGG
+>phiX174_1016_LEFT
+TTCAA
+>phiX174_1016_RIGHT
+CTGGC
+>phiX174_1038_LEFT
+GCCGC
+>phiX174_1038_RIGHT
+TGACC
+>phiX174_1045_LEFT
+GACCT
+>phiX174_1045_RIGHT
+TCCCA
+>phiX174_1048_LEFT
+CTTTC
+>phiX174_1048_RIGHT
+CATCT
+>phiX174_1050_LEFT
+TTCCC
+>phiX174_1050_RIGHT
+TCTTG
+>phiX174_1051_LEFT
+TCCCA
+>phiX174_1051_RIGHT
+CTTGG
+>phiX174_1054_LEFT
+CATCT
+>phiX174_1054_RIGHT
+GGCTT
+>phiX174_1076_LEFT
+AGATT
+>phiX174_1076_RIGHT
+GTCGT
+>phiX174_1080_LEFT
+TGGTC
+>phiX174_1080_RIGHT
+TCTTA
+>phiX174_1092_LEFT
+TACCA
+>phiX174_1092_RIGHT
+TTCAA
+>phiX174_1093_LEFT
+ACCAT
+>phiX174_1093_RIGHT
+TCAAC
+>phiX174_1102_LEFT
+ACTAC
+>phiX174_1102_RIGHT
+CCGGT
+>phiX174_1107_LEFT
+TCCGG
+>phiX174_1107_RIGHT
+TATCG
+>phiX174_1110_LEFT
+GGTTA
+>phiX174_1110_RIGHT
+CGCTG
+>phiX174_1121_LEFT
+GCGAC
+>phiX174_1121_RIGHT
+CCTTC
+>phiX174_1124_LEFT
+ACTCC
+>phiX174_1124_RIGHT
+TCGAG
+>phiX174_1125_LEFT
+CTCCT
+>phiX174_1125_RIGHT
+CGAGA
+>phiX174_1131_LEFT
+CGAGA
+>phiX174_1131_RIGHT
+GGACG
+>phiX174_1141_LEFT
+GCCGT
+>phiX174_1141_RIGHT
+GGCGC
+>phiX174_1145_LEFT
+TTGGC
+>phiX174_1145_RIGHT
+CTCTC
+>phiX174_1147_LEFT
+GGCGC
+>phiX174_1147_RIGHT
+CTCCG
+>phiX174_1149_LEFT
+CGCTC
+>phiX174_1149_RIGHT
+CCGTC
+>phiX174_1156_LEFT
+CGTCT
+>phiX174_1156_RIGHT
+TCTCC
+>phiX174_1159_LEFT
+CTTTC
+>phiX174_1159_RIGHT
+CCATT
+>phiX174_1164_LEFT
+TCCAT
+>phiX174_1164_RIGHT
+GCGTC
+>phiX174_1168_LEFT
+TTGCG
+>phiX174_1168_RIGHT
+CGTGG
+>phiX174_1171_LEFT
+CGTCG
+>phiX174_1171_RIGHT
+GGCCT
+>phiX174_1174_LEFT
+CGTGG
+>phiX174_1174_RIGHT
+CTTGC
+>phiX174_1178_LEFT
+GCCTT
+>phiX174_1178_RIGHT
+CTATT
+>phiX174_1187_LEFT
+TTGAC
+>phiX174_1187_RIGHT
+CTACT
+>phiX174_1189_LEFT
+GACTC
+>phiX174_1189_RIGHT
+ACTGT
+>phiX174_1200_LEFT
+AGACA
+>phiX174_1200_RIGHT
+TTTTA
+>phiX174_1202_LEFT
+ACATT
+>phiX174_1202_RIGHT
+TTACT
+>phiX174_1205_LEFT
+TTTTT
+>phiX174_1205_RIGHT
+CTTTT
+>phiX174_1207_LEFT
+TTTAC
+>phiX174_1207_RIGHT
+TTTTA
+>phiX174_1214_LEFT
+TTTAT
+>phiX174_1214_RIGHT
+TCCCT
+>phiX174_1216_LEFT
+TATGT
+>phiX174_1216_RIGHT
+CCTCA
+>phiX174_1217_LEFT
+ATGTC
+>phiX174_1217_RIGHT
+CTCAT
+>phiX174_1219_LEFT
+GTCCC
+>phiX174_1219_RIGHT
+CATCG
+>phiX174_1223_LEFT
+CTCAT
+>phiX174_1223_RIGHT
+GTCAC
+>phiX174_1227_LEFT
+TCGTC
+>phiX174_1227_RIGHT
+CGTTT
+>phiX174_1232_LEFT
+ACGTT
+>phiX174_1232_RIGHT
+ATGGT
+>phiX174_1236_LEFT
+TTATG
+>phiX174_1236_RIGHT
+TGAAC
+>phiX174_1237_LEFT
+TATGG
+>phiX174_1237_RIGHT
+GAACA
+>phiX174_1240_LEFT
+GGTGA
+>phiX174_1240_RIGHT
+CAGTG
+>phiX174_1245_LEFT
+ACAGT
+>phiX174_1245_RIGHT
+GATTA
+>phiX174_1247_LEFT
+AGTGG
+>phiX174_1247_RIGHT
+TTAAG
+>phiX174_1250_LEFT
+GGATT
+>phiX174_1250_RIGHT
+AGTTC
+>phiX174_1251_LEFT
+GATTA
+>phiX174_1251_RIGHT
+GTTCA
+>phiX174_1253_LEFT
+TTAAG
+>phiX174_1253_RIGHT
+TCATG
+>phiX174_1257_LEFT
+GTTCA
+>phiX174_1257_RIGHT
+GAAGG
+>phiX174_1259_LEFT
+TCATG
+>phiX174_1259_RIGHT
+AGGAT
+>phiX174_1274_LEFT
+TTAAT
+>phiX174_1274_RIGHT
+CCACT
+>phiX174_1277_LEFT
+ATGCC
+>phiX174_1277_RIGHT
+CTCCT
+>phiX174_1279_LEFT
+GCCAC
+>phiX174_1279_RIGHT
+CCTCT
+>phiX174_1284_LEFT
+TCCTC
+>phiX174_1284_RIGHT
+CCCGA
+>phiX174_1289_LEFT
+TCCCG
+>phiX174_1289_RIGHT
+CTGTT
+>phiX174_1296_LEFT
+TGTTA
+>phiX174_1296_RIGHT
+CACTA
+>phiX174_1298_LEFT
+TTAAC
+>phiX174_1298_RIGHT
+CTACT
+>phiX174_1306_LEFT
+ACTGG
+>phiX174_1306_RIGHT
+TATAT
+>phiX174_1307_LEFT
+CTGGT
+>phiX174_1307_RIGHT
+ATATT
+>phiX174_1314_LEFT
+TATTG
+>phiX174_1314_RIGHT
+CCATG
+>phiX174_1317_LEFT
+TGACC
+>phiX174_1317_RIGHT
+TGCCG
+>phiX174_1320_LEFT
+CCATG
+>phiX174_1320_RIGHT
+CGCTT
+>phiX174_1322_LEFT
+ATGCC
+>phiX174_1322_RIGHT
+CTTTT
+>phiX174_1323_LEFT
+TGCCG
+>phiX174_1323_RIGHT
+TTTTC
+>phiX174_1329_LEFT
+TTTTC
+>phiX174_1329_RIGHT
+TGGCA
+>phiX174_1335_LEFT
+TGGCA
+>phiX174_1335_RIGHT
+GATTA
+>phiX174_1338_LEFT
+CACGA
+>phiX174_1338_RIGHT
+TAACC
+>phiX174_1345_LEFT
+AACCC
+>phiX174_1345_RIGHT
+GATAC
+>phiX174_1347_LEFT
+CCCTG
+>phiX174_1347_RIGHT
+TACCA
+>phiX174_1348_LEFT
+CCTGA
+>phiX174_1348_RIGHT
+ACCAA
+>phiX174_1352_LEFT
+ATACC
+>phiX174_1352_RIGHT
+ATAAA
+>phiX174_1354_LEFT
+ACCAA
+>phiX174_1354_RIGHT
+AAAAT
+>phiX174_1359_LEFT
+TAAAA
+>phiX174_1359_RIGHT
+CCCTA
+>phiX174_1366_LEFT
+CCTAA
+>phiX174_1366_RIGHT
+CATTT
+>phiX174_1370_LEFT
+AGCAT
+>phiX174_1370_RIGHT
+TGTTT
+>phiX174_1373_LEFT
+ATTTG
+>phiX174_1373_RIGHT
+TTCAG
+>phiX174_1380_LEFT
+TCAGG
+>phiX174_1380_RIGHT
+TTATT
+>phiX174_1381_LEFT
+CAGGG
+>phiX174_1381_RIGHT
+TATTT
+>phiX174_1384_LEFT
+GGTTA
+>phiX174_1384_RIGHT
+TTGAA
+>phiX174_1385_LEFT
+GTTAT
+>phiX174_1385_RIGHT
+TGAAT
+>phiX174_1391_LEFT
+TGAAT
+>phiX174_1391_RIGHT
+TCTAT
+>phiX174_1393_LEFT
+AATAT
+>phiX174_1393_RIGHT
+TATAA
+>phiX174_1396_LEFT
+ATCTA
+>phiX174_1396_RIGHT
+AACAA
+>phiX174_1397_LEFT
+TCTAT
+>phiX174_1397_RIGHT
+ACAAC
+>phiX174_1400_LEFT
+ATAAC
+>phiX174_1400_RIGHT
+ACTAT
+>phiX174_1401_LEFT
+TAACA
+>phiX174_1401_RIGHT
+CTATT
+>phiX174_1434_LEFT
+CCGTA
+>phiX174_1434_RIGHT
+CGAGG
+>phiX174_1438_LEFT
+ACCGA
+>phiX174_1438_RIGHT
+GCTAA
+>phiX174_1450_LEFT
+CCTAA
+>phiX174_1450_RIGHT
+GAGCT
+>phiX174_1459_LEFT
+CTTAA
+>phiX174_1459_RIGHT
+CAAGA
+>phiX174_1470_LEFT
+TGATG
+>phiX174_1470_RIGHT
+TCGTT
+>phiX174_1484_LEFT
+GTTTC
+>phiX174_1484_RIGHT
+GTTGC
+>phiX174_1487_LEFT
+TCCGT
+>phiX174_1487_RIGHT
+GCTGC
+>phiX174_1491_LEFT
+TTGCT
+>phiX174_1491_RIGHT
+CCATC
+>phiX174_1503_LEFT
+CAAAA
+>phiX174_1503_RIGHT
+CATTT
+>phiX174_1536_LEFT
+GACTG
+>phiX174_1536_RIGHT
+GCTTT
+>phiX174_1541_LEFT
+AGCTT
+>phiX174_1541_RIGHT
+CTCGC
+>phiX174_1553_LEFT
+AAATG
+>phiX174_1553_RIGHT
+CGACT
+>phiX174_1566_LEFT
+TACCA
+>phiX174_1566_RIGHT
+ATCTA
+>phiX174_1572_LEFT
+ATCTA
+>phiX174_1572_RIGHT
+TGACA
+>phiX174_1574_LEFT
+CTATT
+>phiX174_1574_RIGHT
+ACATT
+>phiX174_1575_LEFT
+TATTG
+>phiX174_1575_RIGHT
+CATTA
+>phiX174_1577_LEFT
+TTGAC
+>phiX174_1577_RIGHT
+TTATG
+>phiX174_1581_LEFT
+CATTA
+>phiX174_1581_RIGHT
+GGGTC
+>phiX174_1591_LEFT
+CTGCA
+>phiX174_1591_RIGHT
+GCTGC
+>phiX174_1597_LEFT
+GCTGC
+>phiX174_1597_RIGHT
+TATGC
+>phiX174_1603_LEFT
+TATGC
+>phiX174_1603_RIGHT
+AATTT
+>phiX174_1606_LEFT
+GCTAA
+>phiX174_1606_RIGHT
+TTGCA
+>phiX174_1611_LEFT
+TTTGC
+>phiX174_1611_RIGHT
+TACTG
+>phiX174_1613_LEFT
+TGCAT
+>phiX174_1613_RIGHT
+CTGAC
+>phiX174_1618_LEFT
+ACTGA
+>phiX174_1618_RIGHT
+CAAGA
+>phiX174_1619_LEFT
+CTGAC
+>phiX174_1619_RIGHT
+AAGAA
+>phiX174_1621_LEFT
+GACCA
+>phiX174_1621_RIGHT
+GAACG
+>phiX174_1622_LEFT
+ACCAA
+>phiX174_1622_RIGHT
+AACGT
+>phiX174_1624_LEFT
+CAAGA
+>phiX174_1624_RIGHT
+CGTGA
+>phiX174_1627_LEFT
+GAACG
+>phiX174_1627_RIGHT
+GATTA
+>phiX174_1630_LEFT
+CGTGA
+>phiX174_1630_RIGHT
+TACTT
+>phiX174_1632_LEFT
+TGATT
+>phiX174_1632_RIGHT
+CTTCA
+>phiX174_1634_LEFT
+ATTAC
+>phiX174_1634_RIGHT
+TCATG
+>phiX174_1635_LEFT
+TTACT
+>phiX174_1635_RIGHT
+CATGC
+>phiX174_1639_LEFT
+TTCAT
+>phiX174_1639_RIGHT
+CAGCG
+>phiX174_1645_LEFT
+CAGCG
+>phiX174_1645_RIGHT
+TACCg
+>phiX174_1647_LEFT
+GCGTT
+>phiX174_1647_RIGHT
+CCgTG
+>phiX174_1652_LEFT
+ACCgT
+>phiX174_1652_RIGHT
+ATGTT
+>phiX174_1656_LEFT
+TGATG
+>phiX174_1656_RIGHT
+TATTT
+>phiX174_1658_LEFT
+ATGTT
+>phiX174_1658_RIGHT
+TTTCT
+>phiX174_1659_LEFT
+TGTTA
+>phiX174_1659_RIGHT
+TTCTT
+>phiX174_1663_LEFT
+ATTTC
+>phiX174_1663_RIGHT
+TCATT
+>phiX174_1665_LEFT
+TTCTT
+>phiX174_1665_RIGHT
+ATTTG
+>phiX174_1670_LEFT
+CATTT
+>phiX174_1670_RIGHT
+GAGGT
+>phiX174_1671_LEFT
+ATTTG
+>phiX174_1671_RIGHT
+AGGTA
+>phiX174_1672_LEFT
+TTTGG
+>phiX174_1672_RIGHT
+GGTAA
+>phiX174_1673_LEFT
+TTGGA
+>phiX174_1673_RIGHT
+GTAAA
+>phiX174_1674_LEFT
+TGGAG
+>phiX174_1674_RIGHT
+TAAAA
+>phiX174_1677_LEFT
+AGGTA
+>phiX174_1677_RIGHT
+AACCT
+>phiX174_1678_LEFT
+GGTAA
+>phiX174_1678_RIGHT
+ACCTC
+>phiX174_1682_LEFT
+AAACC
+>phiX174_1682_RIGHT
+CTTAT
+>phiX174_1685_LEFT
+CCTCT
+>phiX174_1685_RIGHT
+ATGAC
+>phiX174_1686_LEFT
+CTCTT
+>phiX174_1686_RIGHT
+TGACG
+>phiX174_1687_LEFT
+TCTTA
+>phiX174_1687_RIGHT
+GACGC
+>phiX174_1688_LEFT
+CTTAT
+>phiX174_1688_RIGHT
+ACGCT
+>phiX174_1689_LEFT
+TTATG
+>phiX174_1689_RIGHT
+CGCTG
+>phiX174_1691_LEFT
+ATGAC
+>phiX174_1691_RIGHT
+CTGAC
+>phiX174_1693_LEFT
+GACGC
+>phiX174_1693_RIGHT
+GACAA
+>phiX174_1695_LEFT
+CGCTG
+>phiX174_1695_RIGHT
+CAACC
+>phiX174_1702_LEFT
+AACCG
+>phiX174_1702_RIGHT
+CCTTT
+>phiX174_1707_LEFT
+TCCTT
+>phiX174_1707_RIGHT
+ACTTG
+>phiX174_1708_LEFT
+CCTTT
+>phiX174_1708_RIGHT
+CTTGT
+>phiX174_1710_LEFT
+TTTAC
+>phiX174_1710_RIGHT
+TGTCA
+>phiX174_1723_LEFT
+CGCTC
+>phiX174_1723_RIGHT
+AATCT
+>phiX174_1724_LEFT
+GCTCT
+>phiX174_1724_RIGHT
+ATCTC
+>phiX174_1725_LEFT
+CTCTA
+>phiX174_1725_RIGHT
+TCTCT
+>phiX174_1726_LEFT
+TCTAA
+>phiX174_1726_RIGHT
+CTCTG
+>phiX174_1730_LEFT
+ATCTC
+>phiX174_1730_RIGHT
+GGGCA
+>phiX174_1739_LEFT
+CATCT
+>phiX174_1739_RIGHT
+GCTAT
+>phiX174_1746_LEFT
+CTATG
+>phiX174_1746_RIGHT
+TGTTG
+>phiX174_1749_LEFT
+TGATG
+>phiX174_1749_RIGHT
+TGATG
+>phiX174_1755_LEFT
+TGATG
+>phiX174_1755_RIGHT
+AACTG
+>phiX174_1756_LEFT
+GATGG
+>phiX174_1756_RIGHT
+ACTGA
+>phiX174_1761_LEFT
+AACTG
+>phiX174_1761_RIGHT
+CCAAA
+>phiX174_1764_LEFT
+TGACC
+>phiX174_1764_RIGHT
+AACGT
+>phiX174_1766_LEFT
+ACCAA
+>phiX174_1766_RIGHT
+CGTCG
+>phiX174_1769_LEFT
+AAACG
+>phiX174_1769_RIGHT
+CGTTA
+>phiX174_1771_LEFT
+ACGTC
+>phiX174_1771_RIGHT
+TTAGG
+>phiX174_1772_LEFT
+CGTCG
+>phiX174_1772_RIGHT
+TAGGC
+>phiX174_1774_LEFT
+TCGTT
+>phiX174_1774_RIGHT
+GGCCA
+>phiX174_1775_LEFT
+CGTTA
+>phiX174_1775_RIGHT
+GCCAG
+>phiX174_1776_LEFT
+GTTAG
+>phiX174_1776_RIGHT
+CCAGT
+>phiX174_1778_LEFT
+TAGGC
+>phiX174_1778_RIGHT
+AGTTT
+>phiX174_1779_LEFT
+AGGCC
+>phiX174_1779_RIGHT
+GTTTT
+>phiX174_1781_LEFT
+GCCAG
+>phiX174_1781_RIGHT
+TTTCT
+>phiX174_1782_LEFT
+CCAGT
+>phiX174_1782_RIGHT
+TTCTG
+>phiX174_1783_LEFT
+CAGTT
+>phiX174_1783_RIGHT
+TCTGG
+>phiX174_1788_LEFT
+TTCTG
+>phiX174_1788_RIGHT
+TCGTG
+>phiX174_1792_LEFT
+GGTCG
+>phiX174_1792_RIGHT
+GTTCA
+>phiX174_1802_LEFT
+AACAG
+>phiX174_1802_RIGHT
+CCTAT
+>phiX174_1804_LEFT
+CAGAC
+>phiX174_1804_RIGHT
+TATAA
+>phiX174_1805_LEFT
+AGACC
+>phiX174_1805_RIGHT
+ATAAA
+>phiX174_1806_LEFT
+GACCT
+>phiX174_1806_RIGHT
+TAAAC
+>phiX174_1824_LEFT
+GCCGC
+>phiX174_1824_RIGHT
+TTTCT
+>phiX174_1825_LEFT
+CCGCG
+>phiX174_1825_RIGHT
+TTCTT
+>phiX174_1833_LEFT
+CTTTG
+>phiX174_1833_RIGHT
+TCCTG
+>phiX174_1843_LEFT
+GAGCA
+>phiX174_1843_RIGHT
+GGCAC
+>phiX174_1847_LEFT
+ATGGC
+>phiX174_1847_RIGHT
+CTATG
+>phiX174_1854_LEFT
+TATGT
+>phiX174_1854_RIGHT
+TACTC
+>phiX174_1860_LEFT
+TACTC
+>phiX174_1860_RIGHT
+TGCGC
+>phiX174_1863_LEFT
+TCTTG
+>phiX174_1863_RIGHT
+GCTTG
+>phiX174_1866_LEFT
+TGCGC
+>phiX174_1866_RIGHT
+TGTTC
+>phiX174_1875_LEFT
+TCGTT
+>phiX174_1875_RIGHT
+TCCGC
+>phiX174_1876_LEFT
+CGTTT
+>phiX174_1876_RIGHT
+CCGCC
+>phiX174_1882_LEFT
+CCGCC
+>phiX174_1882_RIGHT
+ACTGC
+>phiX174_1889_LEFT
+CTGCG
+>phiX174_1889_RIGHT
+CTAAA
+>phiX174_1913_LEFT
+TTAAC
+>phiX174_1913_RIGHT
+CTAAA
+>phiX174_1915_LEFT
+AACGC
+>phiX174_1915_RIGHT
+AAAGG
+>phiX174_1917_LEFT
+CGCTA
+>phiX174_1917_RIGHT
+AGGTG
+>phiX174_1930_LEFT
+TTGAC
+>phiX174_1930_RIGHT
+TATAC
+>phiX174_1934_LEFT
+CTTAT
+>phiX174_1934_RIGHT
+CCGAT
+>phiX174_1940_LEFT
+CCGAT
+>phiX174_1940_RIGHT
+TTGCT
+>phiX174_1942_LEFT
+GATAT
+>phiX174_1942_RIGHT
+GCTGG
+>phiX174_1945_LEFT
+ATTGC
+>phiX174_1945_RIGHT
+GGCGA
+>phiX174_1954_LEFT
+GACCC
+>phiX174_1954_RIGHT
+GTTTT
+>phiX174_1959_LEFT
+TGTTT
+>phiX174_1959_RIGHT
+GTATG
+>phiX174_1994_LEFT
+CTATG
+>phiX174_1994_RIGHT
+AGGAT
+>phiX174_1998_LEFT
+GAAGG
+>phiX174_1998_RIGHT
+TGTTT
diff -r 000000000000 -r 67a4da1a4df3 tool-data/fasta_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample	Thu Mar 19 14:43:10 2015 -0400
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#hg18canon	hg18	Human (Homo sapiens): hg18 Canonical	/depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full	hg18	Human (Homo sapiens): hg18 Full	/depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa
diff -r 000000000000 -r 67a4da1a4df3 tool-data/tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/tool_data_table_conf.xml.sample	Thu Mar 19 14:43:10 2015 -0400
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Location of SAMTools indexes and other files -->
+    <table name="fasta_indexes" comment_char="#">
+        <columns>line_type, value, path</columns>
+        <file path="tool-data/fasta_indexes.loc" />
+    </table>
+</tables>
diff -r 000000000000 -r 67a4da1a4df3 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Mar 19 14:43:10 2015 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="vcflib" version="8a5602bf07">
+        <repository changeset_revision="7e67466b033e" name="package_vcflib_8a5602bf07" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>
diff -r 000000000000 -r 67a4da1a4df3 vcfprimers.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfprimers.xml	Thu Mar 19 14:43:10 2015 -0400
@@ -0,0 +1,67 @@
+<tool id="vcfprimers" name="VCFprimers:" version="0.0.3">
+  <description>Extract flanking sequences for each VCF record</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <expand macro="stdio"></expand>
+  <command>
+    #set $reference_fasta_filename = "localref.fa"
+    #if str( $reference_source.reference_source_selector ) == "history":
+       ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
+    #else:
+       #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
+    #end if    
+   vcfprimers -f "${reference_fasta_filename}" -l "${primer_length}" "${input_vcf}" > "${out_file1}"</command>
+  <inputs>
+<param name="input_vcf" type="data" format="vcf" label="VCF dataset to extract flanks" />
+    <conditional name="reference_source">
+       <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
+         <option value="cached">Locally cached</option>
+         <option value="history">History</option>
+       </param>
+       <when value="cached">
+         <param name="ref_file" type="select" label="Select reference genome">
+           <options from_data_table="fasta_indexes">
+           </options>
+	   <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+         </param>
+       </when>
+       <when value="history"> <!-- FIX ME!!!! -->
+         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+       </when>
+     </conditional>
+     <param name="primer_length" type="integer" value="20" label="The length of the primer sequences on each side of the variant" help="default = 20 bp" />
+  </inputs>
+  <outputs>
+    <data format="fasta" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="reference_source_selector" value="history" />
+      <param name="input_vcf" value="vcflib-phix.vcf"/>
+      <param name="ref_file" value="vcflib-test-genome-phix.fa" />
+      <param name="primer_length" value="5" />
+      <output name="out_file1" file="vcfprimers-test1.fasta"/>
+    </test>
+    </tests>
+  <help>
+
+For each VCF record, extract the flanking sequences, and write them as FASTA
+records suitable for alignment.  This tool is intended for use in designing validation
+experiments.  Primers extracted which would flank all of the alleles at multi-allelic
+sites.  The name of the FASTA "reads" indicates the VCF record which they apply to.
+The form is >CHROM_POS_LEFT for the 3' primer and >CHROM_POS_RIGHT for the 5' primer,
+for example::
+
+ >20_233255_LEFT
+ CCATTGTATATATAGACCATAATTTCTTTATCCAATCATCTGTTGATGGA
+ >20_233255_RIGHT
+ ACTCAGTTGATTCCATACCTTTGCCATCATGAATCATGTTGTAATAAACA
+
+----
+
+Vcfprimers @IS_PART_OF_VCFLIB@
+</help>
+  <expand macro="citations" />
+</tool>